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Releases: SlavovLab/DART-ID

DART-ID v2.0.7

06 May 04:53
@atc3 atc3
v2.0.7
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Thanks to everyone that gave feedback for the first pre-releases of DART-ID. We've made a few changes since the first version packaged with the biorxiv preprint.

v2.0.0

  • Host code on pypi. Now you can install with pip install dart-id
  • Switched from pystan to cmdstan binaries. This obviates bugs and installation troubles associated with pystan but now relies on prebuilt cmdstan binaries for the model. Advanced users modifying the .stan model files will need to build their own binaries (or contact the authors for help doing so)
    • This allows users to also recover parameters from a STAN run that fails to reach an optima given the gradient descent parameters -- something which was not possible with pystan
  • Save protein FDRs from the Fido protein inference algorithm in protein_fdr.txt, along with attaching razor protein FDRs to PSMs in the input data
  • Various robustness fixes that are more resistant to formatting changes in the configuration files
  • figures.html output re-done, and plotting errors fixed
  • Renamed output columns to be more descriptive, also output more diagnostic columns
  • Provide detailed conda environment files for installation/usage from source

v2.0.1

  • Add documentation website https://slavovlab.github.io/DART-ID/
  • Enforce minimum number of confident PSMs per experiment (to avoid accidentally aligning blanks, for example)
  • Add config file with a bunch of sensible default options. These are loaded if the user doesn't specify them
  • Accept DART-ID output files as input files. Just removes the DART-ID columns first
  • Silence pandas deprecation error for pd.concat(...)
  • Add verbosity levels, instead of just true/false
  • More error tolerant figure generation. Now errors in generating figures shouldn't end runs.

v2.0.2

  • Fix installation bug where default config file was not being included

v2.0.3

  • Hotfix crash when loading files without all DART-ID columns.

v2.0.4

  • Hotfix: Add extra filtering step to prevent potential crash during PEP update process.

v2.0.5

  • Validate configuration files with jsonschema

v2.0.6

  • Hotfix: Add missing libwinpthread-1.dll for Windows users without MinGW/msys2 on their path.

v2.0.7 (2019-11-27)

  • Hotfix: Networkx dependency error, when networkx > 2.3
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